6HPW | pdb_00006hpw

Crystal structure of ENL (MLLT1) in complex with compound 20

• PDB DOI: https://doi.org/10.2210/pdb6HPW/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-22 Released: 2018-11-28 
• Deposition Author(s): Heidenreich, D., Chaikuad, A., Moustakim, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Approach toward Identification of Inhibitory Fragments for Eleven-Nineteen-Leukemia Protein (ENL).

Heidenreich, D., Moustakim, M., Schmidt, J., Merk, D., Brennan, P.E., Fedorov, O., Chaikuad, A., Knapp, S.

(2018) J Med Chem 61: 10929-10934

• PubMed: 30407816 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b01457
• Primary Citation of Related Structures:  
  6HPW, 6HPX, 6HPY, 6HPZ, 6HQ0


• PubMed Abstract: 
  

  Lysine acetylation is an epigenetic mark that is principally recognized by bromodomains, and recently structurally diverse YEATS domains also emerged as readers of lysine acetyl/acylations. Here we present a crystallography-based strategy and the discovery of fragments binding to the ENL YEATS domain, a potential drug target. Crystal structures combined with synthetic efforts led to the identification of a submicromolar binder, providing first starting points for the development of chemical probes for this reader domain family.

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Organizational Affiliation: 

Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , 60438 Frankfurt , Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.28 kDa 
• Atom Count: 1,298 
• Modelled Residue Count: 142 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ENL	A	155	Homo sapiens	Mutation(s): 0  Gene Names: MLLT1, ENL, LTG19, YEATS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q03111 (Homo sapiens) Explore Q03111  Go to UniProtKB:  Q03111
PHAROS:  Q03111 GTEx:  ENSG00000130382

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKT	J [auth A]	3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide C21 H23 I N4 O VMKBJIIRNPWSSI-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.738	α = 90
b = 48.738	β = 90
c = 131.623	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Heidenreich, D., Chaikuad, A., Moustakim, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references
• Version 1.2: 2019-04-24
  Changes: Data collection, Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description